8iv5 - Revision history

OCA at 09:43, 14 February 2024

OCA — Wed, 14 Feb 2024 09:43:03 GMT

←Older revision		Revision as of 09:43, 14 February 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]		[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Continual evolution of the SARS-CoV-2 virus has allowed for its gradual evasion of neutralizing antibodies (nAbs) produced in response to natural infection or vaccination. The rapid nature of these changes has incited a need for the development of superior broad nAbs and/or the rational design of an antibody cocktail that can protect against the mutated virus strain. Here, we report two ACE2 competing nAbs-8H12 and 3E2-with synergistic neutralization but evaded by some Omicron subvariants. Cryo-EM reveals the two nAbs synergistic neutralizing virus through a rigorous pairing permitted by rearrangement of the 472-489 loop in the RBD to avoid steric clashing. Bispecific antibodies based on these two nAbs tremendously extend the neutralizing breadth and restore neutralization against recent variants including currently dominant XBB.1.5. Together, these findings expand our understanding of the potential strategies for the neutralization of SARS-CoV-2 variants toward the design of broad-acting antibody therapeutics and vaccines.

-	Two antibodies show broad, synergistic neutralization against SARS-CoV-2 variants by inducing conformational change within the RBD.,Sun H, Deng T, Zhang Y, Lin Y, Jiang Y, Jiang Y, Huang Y, Song S, Cui L, Li T, Xiong H, Lan M, Liu L, Li Y, Fang Q, Yu K, Jiang W, Zhou L, Que Y, Zhang T, Yuan Q, Cheng T, Zhang Z, Yu H, Zhang J, Luo W, Li S, Zheng Q, Gu Y, Xia N Protein Cell. 2023 Jul 20:pwad040. doi: 10.1093/procel/pwad040. PMID:37470320<ref>PMID:37470320</ref>	+	==See Also==
-		+	*[[Spike protein 3D structures\|Spike protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 8iv5" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:26, 16 August 2023

OCA — Wed, 16 Aug 2023 08:26:00 GMT

←Older revision		Revision as of 08:26, 16 August 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8iv5 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 8H12 and 1C4 (local refinement)==
		+	<StructureSection load='8iv5' size='340' side='right'caption='[[8iv5]], [[Resolution\|resolution]] 3.77Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8iv5]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IV5 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.77Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8iv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8iv5 OCA], [https://pdbe.org/8iv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8iv5 RCSB], [https://www.ebi.ac.uk/pdbsum/8iv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8iv5 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Continual evolution of the SARS-CoV-2 virus has allowed for its gradual evasion of neutralizing antibodies (nAbs) produced in response to natural infection or vaccination. The rapid nature of these changes has incited a need for the development of superior broad nAbs and/or the rational design of an antibody cocktail that can protect against the mutated virus strain. Here, we report two ACE2 competing nAbs-8H12 and 3E2-with synergistic neutralization but evaded by some Omicron subvariants. Cryo-EM reveals the two nAbs synergistic neutralizing virus through a rigorous pairing permitted by rearrangement of the 472-489 loop in the RBD to avoid steric clashing. Bispecific antibodies based on these two nAbs tremendously extend the neutralizing breadth and restore neutralization against recent variants including currently dominant XBB.1.5. Together, these findings expand our understanding of the potential strategies for the neutralization of SARS-CoV-2 variants toward the design of broad-acting antibody therapeutics and vaccines.

-	~~Authors:~~ Sun, H., Jiang, Y., ~~Zheng~~, Q., Li, S., ~~Xia~~, N.	+	Two antibodies show broad, synergistic neutralization against SARS-CoV-2 variants by inducing conformational change within the RBD.,Sun H, Deng T, Zhang Y, Lin Y, Jiang Y, Jiang Y, Huang Y, Song S, Cui L, Li T, Xiong H, Lan M, Liu L, Li Y, Fang Q, Yu K, Jiang W, Zhou L, Que Y, Zhang T, Yuan Q, Cheng T, Zhang Z, Yu H, Zhang J, Luo W, Li S, Zheng Q, Gu Y, Xia N Protein Cell. 2023 Jul 20:pwad040. doi: 10.1093/procel/pwad040. PMID:37470320<ref>PMID:37470320</ref>

-	~~Description: Cryo-EM structure~~ of ~~SARS~~-~~CoV~~-~~2 spike protein in complex with double nAbs 8H12 and 1C4 (local refinement)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Li, S~~]]	+	<div class="pdbe-citations 8iv5" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Zheng, Q~~]]	+	== References ==
-	[[Category: Sun, H]]	+	<references/>
-	[[Category: Xia, N]]	+	__TOC__
-	[[Category: ~~Jiang, Y~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mus musculus]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Jiang Y]]
		+	[[Category: Li S]]
		+	[[Category: Sun H]]
		+	[[Category: Xia N]]
		+	[[Category: Zheng Q]]

OCA at 05:26, 3 May 2023

OCA — Wed, 03 May 2023 05:26:21 GMT

←Older revision		Revision as of 05:26, 3 May 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8iv5 is ON HOLD	+	The entry 8iv5 is ON HOLD until Paper Publication

	Authors: Sun, H., Jiang, Y., Zheng, Q., Li, S., Xia, N.		Authors: Sun, H., Jiang, Y., Zheng, Q., Li, S., Xia, N.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Li, S]]		[[Category: Li, S]]
-	[[Category: Xia, N]]
-	[[Category: Jiang, Y]]
	[[Category: Zheng, Q]]		[[Category: Zheng, Q]]
	[[Category: Sun, H]]		[[Category: Sun, H]]
		+	[[Category: Xia, N]]
		+	[[Category: Jiang, Y]]

OCA: Protected "8iv5" [edit=sysop:move=sysop]

OCA — Fri, 07 Apr 2023 05:03:52 GMT

Protected "8iv5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:03, 7 April 2023

OCA: New page: '''Unreleased structure''' The entry 8iv5 is ON HOLD Authors: Sun, H., Jiang, Y., Zheng, Q., Li, S., Xia, N. Description: Cryo-EM structure of SARS-CoV-2 spike protein in complex with ...

OCA — Fri, 07 Apr 2023 05:03:51 GMT

New page: '''Unreleased structure''' The entry 8iv5 is ON HOLD Authors: Sun, H., Jiang, Y., Zheng, Q., Li, S., Xia, N. Description: Cryo-EM structure of SARS-CoV-2 spike protein in complex with ...

New page

'''Unreleased structure'''

The entry 8iv5 is ON HOLD

Authors: Sun, H., Jiang, Y., Zheng, Q., Li, S., Xia, N.

Description: Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 8H12 and 1C4 (local refinement)
[[Category: Unreleased Structures]]
[[Category: Li, S]]
[[Category: Xia, N]]
[[Category: Jiang, Y]]
[[Category: Zheng, Q]]
[[Category: Sun, H]]